I have exactly the same problem, only I've got 10 duplicates of every single shelf (11 different shelves therefore 13 pages of duplicated shelves).

I can't delete them either - all that happens is the books are deleted from the shelves.

The online Kobo Help person told me to do a factory reset. Umm, no thanks. I don't want to lose all my awards (I have them all), or the sideloaded books (altho I do have those on my PC - it's just the hassle of reloading them.)